******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/46/46.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 19541 1.0000 500 20008 1.0000 500 22350 1.0000 500 25242 1.0000 500 26383 1.0000 500 26889 1.0000 500 26893 1.0000 500 27101 1.0000 500 28209 1.0000 500 29531 1.0000 500 30036 1.0000 500 31277 1.0000 500 31796 1.0000 500 32752 1.0000 500 33977 1.0000 500 34368 1.0000 500 38925 1.0000 500 39499 1.0000 500 40669 1.0000 500 42114 1.0000 500 42332 1.0000 500 42457 1.0000 500 5259 1.0000 500 6071 1.0000 500 6363 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/46/46.seqs.fa -oc motifs/46 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 25 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.246 G 0.235 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.246 G 0.235 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 22 llr = 222 E-value = 5.1e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2::6:121:13126 pos.-specific C 832199:9:51914 probability G :1::::::::1::: matrix T :5721:7:a44:7: bits 2.1 1.9 * 1.7 ** ** 1.5 ** ** Relative 1.3 * ** ** * Entropy 1.0 * ** ** * * (14.6 bits) 0.8 * * ***** *** 0.6 * ******** *** 0.4 ********** *** 0.2 ************** 0.0 -------------- Multilevel CTTACCTCTCTCTA consensus ACCT TA AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 40669 406 2.95e-07 AATACGCCGG ATTACCTCTTACTA CAGCGGCATC 6363 426 5.19e-07 ATATTGTGTC CGTACCTCTTACTA CCTTTCACGC 26893 465 5.61e-07 CTACGAGGAG CCTACCACTTACTA CCTCGAACTC 26889 285 5.61e-07 AGCGCCAAAA CCTACCACTTACTA AGGAGGGAGG 38925 22 1.21e-06 ATCCGACCGT CTCTCCTCTCTCTC TCGCAGTCGT 6071 397 1.42e-06 GAAATCTTTT CTTACCTATTACTA TGCGTGTTGG 30036 476 2.01e-06 CGTTCCTCTC CTTCCCTCTCCCTC AGATTTTTAT 19541 89 2.44e-06 TAATAGTATA CTTCCCACTTACTA AACCCTACAT 31277 435 3.71e-06 CTTACCTCTC CTTTCCTCTCTCCC CCTCTTCTAC 22350 477 4.09e-06 CCACCTCGTC CTTATCTCTTCCTA TAGTATTGGT 34368 475 4.51e-06 ACACTTGTTT CTCTCCTCTCTCAC ACATCAAACC 5259 330 5.04e-06 AGTTGCCCCT ACCACCTCTCTCAA GACATCTTTG 26383 458 6.11e-06 CTCCACTCAA CTTTCCTCTCGCCA CAGTACTCTT 25242 121 6.11e-06 CTGTTTGAAC CCTACCTCTTTAAA AGTGATTTGG 20008 446 6.78e-06 CCTCTCCATC CCTACCCCTCTCAA CTCTCTCTTC 39499 429 1.89e-05 CATTCCGCTA CTCACCAATCTCTC TCTCTCTCTC 33977 281 2.56e-05 AGAGTTCCTA CTTCCATCTATCTA TCCACCTCAA 42114 168 3.67e-05 AATCGGCGAT CGTACCTCTCCGTC AAATTGAGAG 29531 445 4.21e-05 TATCGCACTA ACTACCGCTAACTA ATTTCTCACG 27101 478 7.54e-05 CTCCGCAGTT AATTCCTCTCTATA CTCTCTATC 42457 188 9.00e-05 TACTTTCGAA ATCACATCTCGCAC ACCTGCCCAT 42332 36 9.53e-05 TCGCAATGTG CCAATCTCTTGCTC TTTAACTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40669 3e-07 405_[+1]_81 6363 5.2e-07 425_[+1]_61 26893 5.6e-07 464_[+1]_22 26889 5.6e-07 284_[+1]_202 38925 1.2e-06 21_[+1]_465 6071 1.4e-06 396_[+1]_90 30036 2e-06 475_[+1]_11 19541 2.4e-06 88_[+1]_398 31277 3.7e-06 434_[+1]_52 22350 4.1e-06 476_[+1]_10 34368 4.5e-06 474_[+1]_12 5259 5e-06 329_[+1]_157 26383 6.1e-06 457_[+1]_29 25242 6.1e-06 120_[+1]_366 20008 6.8e-06 445_[+1]_41 39499 1.9e-05 428_[+1]_58 33977 2.6e-05 280_[+1]_206 42114 3.7e-05 167_[+1]_319 29531 4.2e-05 444_[+1]_42 27101 7.5e-05 477_[+1]_9 42457 9e-05 187_[+1]_299 42332 9.5e-05 35_[+1]_451 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=22 40669 ( 406) ATTACCTCTTACTA 1 6363 ( 426) CGTACCTCTTACTA 1 26893 ( 465) CCTACCACTTACTA 1 26889 ( 285) CCTACCACTTACTA 1 38925 ( 22) CTCTCCTCTCTCTC 1 6071 ( 397) CTTACCTATTACTA 1 30036 ( 476) CTTCCCTCTCCCTC 1 19541 ( 89) CTTCCCACTTACTA 1 31277 ( 435) CTTTCCTCTCTCCC 1 22350 ( 477) CTTATCTCTTCCTA 1 34368 ( 475) CTCTCCTCTCTCAC 1 5259 ( 330) ACCACCTCTCTCAA 1 26383 ( 458) CTTTCCTCTCGCCA 1 25242 ( 121) CCTACCTCTTTAAA 1 20008 ( 446) CCTACCCCTCTCAA 1 39499 ( 429) CTCACCAATCTCTC 1 33977 ( 281) CTTCCATCTATCTA 1 42114 ( 168) CGTACCTCTCCGTC 1 29531 ( 445) ACTACCGCTAACTA 1 27101 ( 478) AATTCCTCTCTATA 1 42457 ( 188) ATCACATCTCGCAC 1 42332 ( 36) CCAATCTCTTGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 12175 bayes= 9.46526 E= 5.1e-007 -15 165 -1110 -1110 -247 37 -137 103 -247 -12 -1110 144 134 -85 -1110 -23 -1110 188 -1110 -155 -147 188 -1110 -1110 -47 -244 -237 144 -147 188 -1110 -1110 -1110 -1110 -1110 190 -147 102 -1110 61 34 -85 -78 61 -147 181 -237 -1110 -15 -144 -1110 135 134 56 -1110 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 22 E= 5.1e-007 0.227273 0.772727 0.000000 0.000000 0.045455 0.318182 0.090909 0.545455 0.045455 0.227273 0.000000 0.727273 0.636364 0.136364 0.000000 0.227273 0.000000 0.909091 0.000000 0.090909 0.090909 0.909091 0.000000 0.000000 0.181818 0.045455 0.045455 0.727273 0.090909 0.909091 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.090909 0.500000 0.000000 0.409091 0.318182 0.136364 0.136364 0.409091 0.090909 0.863636 0.045455 0.000000 0.227273 0.090909 0.000000 0.681818 0.636364 0.363636 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][TC][TC][AT]CCTCT[CT][TA]C[TA][AC] -------------------------------------------------------------------------------- Time 4.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 25 llr = 258 E-value = 6.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3:21:12:2:2:::1:::311 pos.-specific C :224143:48218::4:1321 probability G :8419227:153:a3275:67 matrix T 7:14:22341262:6534412 bits 2.1 1.9 * 1.7 * 1.5 * ** Relative 1.3 * * ** Entropy 1.0 ** * * * ** * (14.9 bits) 0.8 ** * * * ** * 0.6 ** * * * *** ** * 0.4 ** * * * ********** 0.2 ****** ************** 0.0 --------------------- Multilevel TGGCGCCGCCGTCGTTGGTGG consensus A AT GATT TG GCTTAC sequence C TG A C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 42457 296 5.53e-08 CAGTGTTGGT TGACGTCGTCGTCGGCGTTGT TTGTTTGAAA 28209 286 6.49e-08 AGAGACGACC TGTCGCCGACTTCGGTGTAGG TTTGCTGCCG 32752 202 3.23e-07 TTTTTGAGTG TGGTGGCGACGGCGATGCTGG GATTCGCGGA 31277 199 3.23e-07 AGGCAGACGC TCGTGTAGTCGGCGTCGGACG TCCTCCTCCC 38925 140 4.21e-07 TGTGCTCATT AGCCGCTGTCGTCGTCGTCGC CTCTCGCAAC 19541 296 4.79e-07 AACGGTCTCG TGGCGTCTTCTCCGTCTGAGG GTGCAACAAG 5259 290 1.27e-06 CGAGAGAGTA TGGGGCATTGTGCGTCGGTGG CGTGTGCTTA 42114 284 1.99e-06 ATGTGCCACA AGACGCGTCTGTCGGTGGCCG TAGCTTGGAT 31796 336 1.99e-06 GACGGTAGTT TGGCGTAGACGTTGGGTGTCG ATGGTGGTTG 40669 37 2.47e-06 AGGCGTTCGC TCGTGGTGCCCGCGTTGGCTG ATGATCGGCC 39499 385 2.75e-06 TCATTCCACA AGTCGATGCCCTCGTTGGTAG TTTGCTTCCC 26383 171 2.75e-06 CTTGTCGAGG AGGTGCGTTCGACGATGGCGG TGCCGACCAC 33977 252 3.05e-06 ATGGTTCATG TGGTGTGTATTTCGTTGGTAG AGTTCCTACT 34368 122 3.38e-06 GACGTGCGGC AGCCGCCGCCGTCGTGGTCAC TACACCATGA 27101 207 4.14e-06 TGTGGTTTTA TCCTGCCGTCGGCGTGGTTCT GGCGACGATA 6071 91 8.11e-06 TCTGCAGCCA ATGCGGAGTCGTCGTTTGAGT TTTCGCCTTG 26893 33 8.11e-06 TCGTTCATCA TGCTCTGGGCATCGTTGTAGG TGGGAGTTGA 22350 140 9.72e-06 GTGAGCGCCA TGACGATGCCACCGGCTGCCG ATTAAGGGTA 29531 201 1.38e-05 GAGGTTGTTG TGTTGGAGAGCTCGAGGGTGG GTGGGTGGGC 30036 34 3.07e-05 TTCGACGTGG TGGAGAGGCTTGCGGTGGCGA TGGGGGCCGA 25242 196 3.56e-05 TGTTTAGTGT TGCGGCGGTCACTGTCGTTGA CTTGGAGAGC 6363 42 3.83e-05 AAGCCTACAA AGAAGGTGCCATCGTTTCAGT TCCAGCCAGC 20008 353 5.44e-05 TTGCATTGTA TGCAGGATCCCTTGGCTTTTG TGTGGCGTCG 42332 169 8.58e-05 AAGTGAGGTG TGATCCCTCGGTTGTTTTATG AGAAGGGATA 26889 122 2.70e-04 ATCACTACGA TCAGCCCTACGGCAGCTTTGG CACAATGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42457 5.5e-08 295_[+2]_184 28209 6.5e-08 285_[+2]_194 32752 3.2e-07 201_[+2]_278 31277 3.2e-07 198_[+2]_281 38925 4.2e-07 139_[+2]_340 19541 4.8e-07 295_[+2]_184 5259 1.3e-06 289_[+2]_190 42114 2e-06 283_[+2]_196 31796 2e-06 335_[+2]_144 40669 2.5e-06 36_[+2]_443 39499 2.7e-06 384_[+2]_95 26383 2.7e-06 170_[+2]_309 33977 3.1e-06 251_[+2]_228 34368 3.4e-06 121_[+2]_358 27101 4.1e-06 206_[+2]_273 6071 8.1e-06 90_[+2]_389 26893 8.1e-06 32_[+2]_447 22350 9.7e-06 139_[+2]_340 29531 1.4e-05 200_[+2]_279 30036 3.1e-05 33_[+2]_446 25242 3.6e-05 195_[+2]_284 6363 3.8e-05 41_[+2]_438 20008 5.4e-05 352_[+2]_127 42332 8.6e-05 168_[+2]_311 26889 0.00027 121_[+2]_358 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=25 42457 ( 296) TGACGTCGTCGTCGGCGTTGT 1 28209 ( 286) TGTCGCCGACTTCGGTGTAGG 1 32752 ( 202) TGGTGGCGACGGCGATGCTGG 1 31277 ( 199) TCGTGTAGTCGGCGTCGGACG 1 38925 ( 140) AGCCGCTGTCGTCGTCGTCGC 1 19541 ( 296) TGGCGTCTTCTCCGTCTGAGG 1 5259 ( 290) TGGGGCATTGTGCGTCGGTGG 1 42114 ( 284) AGACGCGTCTGTCGGTGGCCG 1 31796 ( 336) TGGCGTAGACGTTGGGTGTCG 1 40669 ( 37) TCGTGGTGCCCGCGTTGGCTG 1 39499 ( 385) AGTCGATGCCCTCGTTGGTAG 1 26383 ( 171) AGGTGCGTTCGACGATGGCGG 1 33977 ( 252) TGGTGTGTATTTCGTTGGTAG 1 34368 ( 122) AGCCGCCGCCGTCGTGGTCAC 1 27101 ( 207) TCCTGCCGTCGGCGTGGTTCT 1 6071 ( 91) ATGCGGAGTCGTCGTTTGAGT 1 26893 ( 33) TGCTCTGGGCATCGTTGTAGG 1 22350 ( 140) TGACGATGCCACCGGCTGCCG 1 29531 ( 201) TGTTGGAGAGCTCGAGGGTGG 1 30036 ( 34) TGGAGAGGCTTGCGGTGGCGA 1 25242 ( 196) TGCGGCGGTCACTGTCGTTGA 1 6363 ( 42) AGAAGGTGCCATCGTTTCAGT 1 20008 ( 353) TGCAGGATCCCTTGGCTTTTG 1 42332 ( 169) TGATCCCTCGGTTGTTTTATG 1 26889 ( 122) TCAGCCCTACGGCAGCTTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 8.90388 E= 6.7e-005 15 -1129 -1129 143 -1129 -62 177 -274 -7 -4 77 -115 -107 70 -97 43 -1129 -104 191 -1129 -107 70 3 -15 -7 38 3 -42 -1129 -1129 153 26 -7 55 -255 43 -1129 163 -97 -115 -65 -62 103 -42 -265 -104 25 107 -1129 177 -1129 -74 -265 -1129 203 -1129 -107 -1129 45 107 -1129 55 -55 84 -1129 -1129 153 26 -1129 -162 115 58 15 18 -1129 72 -107 -30 125 -115 -165 -162 153 -74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 25 E= 6.7e-005 0.280000 0.000000 0.000000 0.720000 0.000000 0.160000 0.800000 0.040000 0.240000 0.240000 0.400000 0.120000 0.120000 0.400000 0.120000 0.360000 0.000000 0.120000 0.880000 0.000000 0.120000 0.400000 0.240000 0.240000 0.240000 0.320000 0.240000 0.200000 0.000000 0.000000 0.680000 0.320000 0.240000 0.360000 0.040000 0.360000 0.000000 0.760000 0.120000 0.120000 0.160000 0.160000 0.480000 0.200000 0.040000 0.120000 0.280000 0.560000 0.000000 0.840000 0.000000 0.160000 0.040000 0.000000 0.960000 0.000000 0.120000 0.000000 0.320000 0.560000 0.000000 0.360000 0.160000 0.480000 0.000000 0.000000 0.680000 0.320000 0.000000 0.080000 0.520000 0.400000 0.280000 0.280000 0.000000 0.440000 0.120000 0.200000 0.560000 0.120000 0.080000 0.080000 0.680000 0.160000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA]G[GAC][CT]G[CGT][CAGT][GT][CTA]C[GT][TG]CG[TG][TC][GT][GT][TAC][GC]G -------------------------------------------------------------------------------- Time 9.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 20 llr = 201 E-value = 2.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 45932a917392997 pos.-specific C 45:48::427:5222 probability G 1:111::::::2::2 matrix T 11:31:262112::: bits 2.1 * 1.9 * 1.7 * 1.5 * ** * ** Relative 1.3 * ** * ** Entropy 1.0 * ** * ** (14.5 bits) 0.8 ** *** *** *** 0.6 ** ******* *** 0.4 ** ******* *** 0.2 *************** 0.0 --------------- Multilevel ACACCAATACACAAA consensus CA A C A G C sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 29531 61 5.94e-09 CCCCGCCACC ACAACAATACACAAA TACTAGCCCT 42114 485 1.41e-08 CACAGCTCCT CAATCAATACACAAA A 31277 472 4.38e-07 CCAAAAACAG AAATCAATAAATAAA CCGAATATCC 32752 102 8.75e-07 TTTGTGCACA ACACCAACACAGCAA CCATGGTTAT 26889 53 2.25e-06 AGCAGCCTAC ACAGCAACACACAAC ATCGGCAACT 26383 485 2.25e-06 TACTCTTTAT ACACAAATAAATAAA C 19541 486 3.39e-06 CGTTACTACT CAAACATAACACAAA 30036 305 3.76e-06 TGAACCCTTG CCAAAATCACACAAA CGCCCTCCAA 42332 471 4.65e-06 CCCAATCAAA CAAACAAAACAGAAG TCACGGCGTG 39499 74 8.44e-06 CCCCCACTTC CCGCCAATTCATAAA GTATCCAGAA 33977 9 1.52e-05 CAGACAAA CCGACAATACTGAAA GAGTGAACGA 25242 240 1.52e-05 GATCAACAGT TAACCAATCAACAAC GTGACATACT 22350 105 1.79e-05 ACCTTACCAG CAACCAACATTCAAA GCAACTTGAG 28209 356 2.49e-05 ATCTGCGGGC AAATCAATTCAGCAG CTTCTACGCT 38925 338 2.69e-05 TGTCGCTGTC GAACAAATACAAACA CCCTGCATGC 42457 83 3.12e-05 CCCGTACAAT GCATCATCAAACAAG GAAGATCTAC 20008 484 4.43e-05 CTCAGTTGAC ATATTAATACAAAAA AA 6071 470 4.74e-05 ACTCATCACC ACAACAACTCAACCA CATCAACACC 31796 205 5.80e-05 TTTTCACTAG CAACGAACCAACAAC TCGTTCAAGA 27101 403 6.19e-05 CTGTCAAATC TCATCAATCCATACC GACACACTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29531 5.9e-09 60_[+3]_425 42114 1.4e-08 484_[+3]_1 31277 4.4e-07 471_[+3]_14 32752 8.8e-07 101_[+3]_384 26889 2.2e-06 52_[+3]_433 26383 2.2e-06 484_[+3]_1 19541 3.4e-06 485_[+3] 30036 3.8e-06 304_[+3]_181 42332 4.7e-06 470_[+3]_15 39499 8.4e-06 73_[+3]_412 33977 1.5e-05 8_[+3]_477 25242 1.5e-05 239_[+3]_246 22350 1.8e-05 104_[+3]_381 28209 2.5e-05 355_[+3]_130 38925 2.7e-05 337_[+3]_148 42457 3.1e-05 82_[+3]_403 20008 4.4e-05 483_[+3]_2 6071 4.7e-05 469_[+3]_16 31796 5.8e-05 204_[+3]_281 27101 6.2e-05 402_[+3]_83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=20 29531 ( 61) ACAACAATACACAAA 1 42114 ( 485) CAATCAATACACAAA 1 31277 ( 472) AAATCAATAAATAAA 1 32752 ( 102) ACACCAACACAGCAA 1 26889 ( 53) ACAGCAACACACAAC 1 26383 ( 485) ACACAAATAAATAAA 1 19541 ( 486) CAAACATAACACAAA 1 30036 ( 305) CCAAAATCACACAAA 1 42332 ( 471) CAAACAAAACAGAAG 1 39499 ( 74) CCGCCAATTCATAAA 1 33977 ( 9) CCGACAATACTGAAA 1 25242 ( 240) TAACCAATCAACAAC 1 22350 ( 105) CAACCAACATTCAAA 1 28209 ( 356) AAATCAATTCAGCAG 1 38925 ( 338) GAACAAATACAAACA 1 42457 ( 83) GCATCATCAAACAAG 1 20008 ( 484) ATATTAATACAAAAA 1 6071 ( 470) ACAACAACTCAACCA 1 31796 ( 205) CAACGAACCAACAAC 1 27101 ( 403) TCATCAATCCATACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 12150 bayes= 9.49628 E= 2.9e-001 67 70 -123 -142 84 102 -1097 -241 184 -1097 -123 -1097 25 51 -223 17 -75 161 -223 -241 199 -1097 -1097 -1097 176 -1097 -1097 -83 -133 51 -1097 104 148 -72 -1097 -83 -1 151 -1097 -241 184 -1097 -1097 -142 -75 87 -23 -42 176 -72 -1097 -1097 176 -72 -1097 -1097 137 -30 -65 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 20 E= 2.9e-001 0.400000 0.400000 0.100000 0.100000 0.450000 0.500000 0.000000 0.050000 0.900000 0.000000 0.100000 0.000000 0.300000 0.350000 0.050000 0.300000 0.150000 0.750000 0.050000 0.050000 1.000000 0.000000 0.000000 0.000000 0.850000 0.000000 0.000000 0.150000 0.100000 0.350000 0.000000 0.550000 0.700000 0.150000 0.000000 0.150000 0.250000 0.700000 0.000000 0.050000 0.900000 0.000000 0.000000 0.100000 0.150000 0.450000 0.200000 0.200000 0.850000 0.150000 0.000000 0.000000 0.850000 0.150000 0.000000 0.000000 0.650000 0.200000 0.150000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC][CA]A[CAT]CAA[TC]A[CA]A[CGT]AA[AC] -------------------------------------------------------------------------------- Time 14.31 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19541 1.14e-07 88_[+1(2.44e-06)]_193_\ [+2(4.79e-07)]_169_[+3(3.39e-06)] 20008 1.84e-04 352_[+2(5.44e-05)]_58_\ [+1(1.35e-05)]_[+1(6.78e-06)]_24_[+3(4.43e-05)]_2 22350 1.21e-05 104_[+3(1.79e-05)]_20_\ [+2(9.72e-06)]_316_[+1(4.09e-06)]_10 25242 4.65e-05 120_[+1(6.11e-06)]_61_\ [+2(3.56e-05)]_23_[+3(1.52e-05)]_246 26383 8.80e-07 170_[+2(2.75e-06)]_197_\ [+1(4.51e-05)]_55_[+1(6.11e-06)]_13_[+3(2.25e-06)]_1 26889 5.97e-06 52_[+3(2.25e-06)]_26_[+3(7.51e-05)]_\ 176_[+1(5.61e-07)]_202 26893 8.79e-05 32_[+2(8.11e-06)]_411_\ [+1(5.61e-07)]_22 27101 2.11e-04 206_[+2(4.14e-06)]_175_\ [+3(6.19e-05)]_60_[+1(7.54e-05)]_9 28209 1.34e-05 285_[+2(6.49e-08)]_49_\ [+3(2.49e-05)]_130 29531 9.94e-08 60_[+3(5.94e-09)]_125_\ [+2(1.38e-05)]_223_[+1(4.21e-05)]_42 30036 4.46e-06 33_[+2(3.07e-05)]_231_\ [+1(9.00e-05)]_5_[+3(3.76e-06)]_156_[+1(2.01e-06)]_11 31277 1.80e-08 167_[+2(7.56e-05)]_10_\ [+2(3.23e-07)]_3_[+2(4.74e-05)]_172_[+3(9.57e-05)]_4_[+1(3.71e-06)]_23_\ [+3(4.38e-07)]_14 31796 1.42e-03 204_[+3(5.80e-05)]_116_\ [+2(1.99e-06)]_144 32752 8.33e-06 101_[+3(8.75e-07)]_85_\ [+2(3.23e-07)]_278 33977 1.90e-05 8_[+3(1.52e-05)]_228_[+2(3.05e-06)]_\ 8_[+1(2.56e-05)]_206 34368 1.65e-04 121_[+2(3.38e-06)]_332_\ [+1(4.51e-06)]_12 38925 3.51e-07 21_[+1(1.21e-06)]_104_\ [+2(4.21e-07)]_177_[+3(2.69e-05)]_148 39499 7.87e-06 73_[+3(8.44e-06)]_296_\ [+2(2.75e-06)]_23_[+1(1.89e-05)]_58 40669 1.69e-05 36_[+2(2.47e-06)]_348_\ [+1(2.95e-07)]_81 42114 3.30e-08 167_[+1(3.67e-05)]_102_\ [+2(1.99e-06)]_180_[+3(1.41e-08)]_1 42332 3.73e-04 35_[+1(9.53e-05)]_119_\ [+2(8.58e-05)]_281_[+3(4.65e-06)]_15 42457 3.06e-06 82_[+3(3.12e-05)]_90_[+1(9.00e-05)]_\ 94_[+2(5.53e-08)]_184 5259 5.21e-05 289_[+2(1.27e-06)]_19_\ [+1(5.04e-06)]_157 6071 9.51e-06 90_[+2(8.11e-06)]_285_\ [+1(1.42e-06)]_59_[+3(4.74e-05)]_16 6363 2.55e-04 41_[+2(3.83e-05)]_363_\ [+1(5.19e-07)]_61 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************